Alignments for a candidate for manA in Roseburia faecis M72

GapMind for catabolism of small carbon sources

Alignments for a candidate for manA in Roseburia faecis M72

Align Mannose-6-phosphate isomerase ManA; Phosphohexomutase; Phosphomannose isomerase; PMI; EC 5.3.1.8 (characterized)
to candidate WP_055067486.1 M72_RS05525 GH1 family beta-glucosidase

Query= SwissProt::O31646
         (315 letters)



>NCBI__GCF_001406815.1:WP_055067486.1
          Length = 770

 Score =  314 bits (804), Expect = 5e-90
 Identities = 155/310 (50%), Positives = 200/310 (64%), Gaps = 7/310 (2%)

Query: 6   LFFKPVFKERIWGGTALAD-FGYTIPSQRTGECWAFAAHQNGQSVVQNGMYKGFTLSELW 64
           LF +PVF   IWGGT L + +GY+I     GECW  AAH NG   + +G YK   LS+LW
Sbjct: 461 LFMEPVFTHNIWGGTKLREEYGYSIEGDDIGECWGIAAHPNGTCTIADGAYKEKKLSDLW 520

Query: 65  EHHRHLFGQLEGDRFPLLTKILDADQDLSVQVHPNDEYANIHENGELGKTECWYIIDCQK 124
           E HR LFG  +G  FPLL KI+DA  DLS+QVHP+D YA  HE G LGK ECWYI+DC+ 
Sbjct: 521 EEHRELFGNTQGKVFPLLIKIIDAKADLSIQVHPDDTYAAEHEKGSLGKMECWYILDCEP 580

Query: 125 DAEIIYGHNATTKEELTTMIERGEWDELLRRVKVKPGDFFYVPSGTVHAIGKGILALETQ 184
           D++++ GHNA T EEL  M+  G W EL+R V VK GDF  +  GTVHAI  GI  LETQ
Sbjct: 581 DSKLVIGHNAKTHEELEDMVHNGRWSELIREVPVKKGDFIQIDPGTVHAIKGGITILETQ 640

Query: 185 QNSDTTYRLYDYDRKDAEGKLRELHLKKSIEVIEVPSIP-ERHTVHHEQIEDLLTTTLIE 243
           QNSD TYR+YDYDR  + GK R+LH+++S++VI+VP+ P     +   + E      LIE
Sbjct: 641 QNSDITYRVYDYDRL-SNGKPRQLHIQQSLDVIKVPAAPLSECMIKTGEAEANKLQKLIE 699

Query: 244 CAYFSVGKWNLSGSASLKQQKPFLLISVIEGEGRMISGEYVYPFKKGDHMLLPYGLGEFK 303
           C Y+ V    + G A  +Q+ PFL++SV+EG G +         KKGDH +LPY  G+ +
Sbjct: 700 CKYYQVFHMKVEGQAEFEQEYPFLIVSVVEGNGLLNHTS----VKKGDHFILPYDYGKVE 755

Query: 304 LEGYAECIVS 313
           +EG  E + S
Sbjct: 756 IEGNLEFVAS 765


Lambda     K      H
   0.319    0.138    0.425 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 812
Number of extensions: 49
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 315
Length of database: 770
Length adjustment: 34
Effective length of query: 281
Effective length of database: 736
Effective search space:   206816
Effective search space used:   206816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_055067486.1 M72_RS05525 (GH1 family beta-glucosidase)
to HMM TIGR00218 (manA: mannose-6-phosphate isomerase, class I (EC 5.3.1.8))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00218.hmm
# target sequence database:        /tmp/gapView.2349002.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00218  [M=359]
Accession:   TIGR00218
Description: manA: mannose-6-phosphate isomerase, class I
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.3e-70  224.3   0.1    7.5e-41  126.4   0.0    2.1  2  NCBI__GCF_001406815.1:WP_055067486.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001406815.1:WP_055067486.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.0   3.7e-32   3.7e-32       3     102 ..     462     557 ..     460     564 .. 0.91
   2 !  126.4   0.0   7.5e-41   7.5e-41     142     358 ..     557     765 ..     556     766 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 3.7e-32
                             TIGR00218   3 flfrvqknlkerdWGkgtaladllgysipskqtaElWag.aHkkgsSkvqng..kkvsLrdliekhksellGk 72 
                                           f+++v+    + +WG gt+l++ +gysi++  ++E+W + aH++g  +++ g  k++ L+dl+e+h+ el+G+
  NCBI__GCF_001406815.1:WP_055067486.1 462 FMEPVFT---HNIWG-GTKLREEYGYSIEGDDIGECWGIaAHPNGTCTIADGayKEKKLSDLWEEHR-ELFGN 529
                                           5677777...88***.***********************************77999***********.***** PP

                             TIGR00218  73 aeadrfelPlLvkvLsaekplsiqvHPdka 102
                                            ++++  +PlL+k+++a+ +lsiqvHPd  
  NCBI__GCF_001406815.1:WP_055067486.1 530 TQGKV--FPLLIKIIDAKADLSIQVHPDDT 557
                                           *****..*********************33 PP

  == domain 2  score: 126.4 bits;  conditional E-value: 7.5e-41
                             TIGR00218 142 riaelheeaerlgkteawviiasdekikeaaeilkealknskeelkekiqrliypedvglfkgllLnrvklkp 214
                                            +a  he++  lgk+e+w+i +++     + +++ +++++++eel  ++       + g ++ +l++ v +k 
  NCBI__GCF_001406815.1:WP_055067486.1 557 TYAAEHEKGS-LGKMECWYILDCEP----DSKLVIGHNAKTHEELEDMV------HN-GRWS-ELIREVPVKK 616
                                           6788899999.**************....********************......77.****.********** PP

                             TIGR00218 215 geaiyvrsgtvHAy.kggdvlEvmanSdnvvragltd.......kyldvkklvevltveekpeeklkeqkqke 279
                                           g++i + +gtvHA+  g+ +lE+++nSd ++r++++d       + l++++++ v++v++ p ++   +  + 
  NCBI__GCF_001406815.1:WP_055067486.1 617 GDFIQIDPGTVHAIkGGITILETQQNSDITYRVYDYDrlsngkpRQLHIQQSLDVIKVPAAPLSECMIKTGEA 689
                                           **************55679*******************************************99987665444 PP

                             TIGR00218 280 .gaevlflvpieefavlktdlsekaelksqdsalillvleGdglilsgekklklkkGesfliaakleevtieg 351
                                              +++ l+++++++v +++++++ae++++ ++li++v+eG+gl+ +      +kkG++f+++++ ++v+ieg
  NCBI__GCF_001406815.1:WP_055067486.1 690 eANKLQKLIECKYYQVFHMKVEGQAEFEQEYPFLIVSVVEGNGLLNH----TSVKKGDHFILPYDYGKVEIEG 758
                                           25588999***********************************9965....579******************* PP

                             TIGR00218 352 edealvs 358
                                           + e+++s
  NCBI__GCF_001406815.1:WP_055067486.1 759 NLEFVAS 765
                                           *998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (359 nodes)
Target sequences:                          1  (770 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 16.43
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources